JAKARTA — It is a seemingly unending conflict in a part of the world famous for both its awesome remoteness and the incredible wealth on and beneath the ground.

For half a century, Indonesian troops and police officers have fought a shadowy and sporadic war in the vast forests and highlands of Papua, as the western end of New Guinea is known, after taking control of the former Dutch colony in the 1960s. It is a long-running conflict that is poorly understood by even those involved.

On one level, the fight is between security forces and ragtag groups of indigenous separatists, armed with guns, spears and arrows.

Sometimes, it is alleged, it is factions of the security forces fighting among themselves, drawn into competition over the ill-gotten spoils of a region of vast natural resources, including some of the world’s richest mines. Often, official references to those doing the killing go no further than “unknown persons,” leaving their identity — agents provocateurs, business rivals or guerrillas — the stuff of conspiracy theories.

But after an outburst of violence in recent months that has killed dozens, Indonesia is coming under renewed calls to solve a conflict, replete with economic misery and human rights abuses, that has tainted the country’s image as an emerging democratic giant.

A report this week by the International Crisis Group, an independent research organization, is the latest in a series of calls by civil society groups for a renewed dialogue between Papuans, who are ethnically distinct from other Indonesians and many of whom favor independence, and officials in Jakarta, who see the region as an inviolable part of Indonesia.

At issue are special autonomy arrangements put in place a decade ago by the administration of former President Megawati Sukarnoputri to head off renewed calls for independence following the 1998 fall of the Suharto dictatorship. Suharto ruled Papua with an iron fist while making billions for Jakarta from its natural wealth.

Special autonomy devolved some power to Papuans and saw the creation of local governments and the pumping of huge sums of money back into the region. The government also, controversially, split Papua into two separate provinces, Papua and West Papua.

But the report argues that special autonomy has so far failed to solve the roots of the conflict. Deep poverty persists, as does chronic corruption.

Non-Papuan migrants from other parts of Indonesia dominate the economy.

And, importantly, there remains a sense among Papuans that Indonesian security forces remain a law unto themselves, killing and torturing with near impunity.

“The government of President Yudhoyono, on Papua as on everything else, has been glacially slow to develop a policy that would be different from the default response of throwing cash at the problem and hoping it will go away,” the report by the crisis group said.

While democratic Indonesia has made huge strides in solving bloody wars of separatism and intercommunal conflict in provinces like Aceh and Maluku, Papua has stood out as a weeping sore.

Recent violence exposes the complexity of the conflict. The past two months have seen a rash of attacks in the highland district of Puncak Jaya, one of the poorest and remotest areas of Indonesia and a hot spot for a local insurgency led by a faction of the separatist Free Papua Movement, or TPN-OPM.

This month, a helicopter carrying a shot and dying soldier was hit by rebel bullets in the region and, last week, a motorcycle taxi driver was shot and killed in the district capital by “unknown persons,” said Lt. Col. Alex Korwa, the local police chief.

Over the hills, in Puncak, another district created as part of the government’s special autonomy plan, fighting between indigenous clans over control of the local government left 17 dead in late July.

This month, five people, including two soldiers, were killed in separate incidents near Jayapura, the capital of Papua Province. A series of other gunfights and stabbings have continued throughout Papua over this period.

The authorities have, mostly, pointed the finger at the TPN-OPM for the deadliest of the Jayapura attacks, an ambush in which four people were killed. But Papuan independence campaigners assert that elements of the security forces, or their clients, are behind many such attacks.

“These attacks I think have been carried out either by militias, or the military themselves, as violence to create an atmosphere of fear,” said Benny Giay, a pastor in the Gospel Tabernacle Church. The commander of military forces in Papua, Maj. Gen. Erfi Triassunu, said the attack near Jayapura was “purely the TPN-OPM.”

Mr. Giay also alleged that a Papuan farmer, Das Komba, was abducted and killed by soldiers near the border with Papua New Guinea on Friday, but the police and military have so far not commented on the case.

Cases in which members of the security forces received light sentences for the torture and murder of civilians have caused outrage in recent months, but the crisis group argues in its report that the fact such trials exist at all is a step forward.

With Papua thousands of kilometers from Jakarta, and tightly sealed from foreign journalists and many rights groups, it is difficult to confirm independently claims and counterclaims about much of the violence. For those on the ground, too, many attacks remain mysterious.

“How can we trust the police or the military if there are no perpetrators, if no one gets caught?” asked Latifah Anum Siregar, the director of the Democracy Alliance for Papua, a human rights group.

“Police will send out 200, 300 people on a sweep, but they won’t get anyone.”

One senior police officer who has had command roles in Papua’s hot spots said that even he was often uncertain who exactly was behind attacks — rebels or rogue soldiers. “We weren’t sure,” said the officer, who declined to be named because of the sensitivity of the subject. “Every time we got a glance of the shooter, they always disappeared really quickly into the jungle.”

Realizing the drawbacks of special autonomy, the government of President Susilo Bambang Yudhoyono has pledged to put together a temporary body, called the Unit for the Acceleration of Development in Papua and West Papua, to seek solutions to corruption, poverty and rights abuses in the region, but its formation has been delayed.

“There’s a lot of mistrust by the people in Papua, both towards the government in Jakarta and their own regional governments,” said Dewi Fortuna Anwar, a political science professor at the Indonesian Institute of Sciences who is involved in setting up the body.

But building trust may take more than building schools. Many Papuans remain fiercely committed to independence, arguing that the process by which Indonesia achieved sovereignty over Papua in 1969 — a vote by 1,025 Papuan elders handpicked by the Indonesian authorities — was flawed.

Indonesia is similarly inflexible. Simply unfurling the region’s Morning Star independence flag can be considered subversion, a crime punishable by up to 20 years or life in prison. About two dozen people are in jail or awaiting trial in Papua on subversion charges, according to Human Rights Watch.

Amid violence earlier this month, thousands of people protested in Papuan towns and cities to demand a referendum on independence. The political affairs minister, Djoko Suyanto, was firm in his response. “Papua is a part of the unitary republic of Indonesia,” he said. “That is what we must maintain.”